Table 2.

Glossary of Terms Used to Describe Primary Data in the Paper, in the Figures, and in Table 1.

Primary Data Type	Definition
16S rRNA gene survey	Sequence-based analysis of 16S ribosomal RNA gene in total DNA extracts; the data are used to develop microbial community compositional profiles.
Whole metagenome shotgun sequences	Sequence-based analysis of all genes in total DNA extracts; the data are used to develop microbial community compositional, functional, and genomic profiles.
Whole metatranscriptome shotgun sequences	Sequence-based analysis of RNA transcripts in a microbial community by converting RNA in total RNA extracts to complementary DNA and sequencing the cDNA.
Whole virome shotgun sequences	Sequence-based analysis of all virus genes and genomes used to develop viral community profiles. These sequence data are derived from two approaches, either by first isolating viral-sized particles from a sample and then sequencing this fraction, or by sequencing the DNA (or cDNA from RNA) extract and computationally determining DNA and RNA viral sequences in the metagenome.
Bacterial isolates	Isolation and cultivation of a specific bacterium in a mixed community through the use of selective media or enrichment techniques to preferentially grow one bacterium of interest.
Single-cell genome sequences	Physical separation or physical enrichment of a single microbial cell from a mixed population of cells. Sequence-based analysis of the single cell’s genome is conducted using a DNA random priming method to first increase the total DNA concentration in the cell and subsequently sequence this amplified DNA.
Single-cell RNA sequences	Sequence-based analysis of RNA transcripts in a cell by converting RNA in total RNA extracts to complementary DNA and sequencing the cDNA.
LC-MS/MS peptide profiles	Analysis of individual peptides in a mixture of proteins by a combination of liquid chromatography and mass spectroscopy after enzymatic digestion of the protein mixture. To derive the microbiome metaproteome, data from the companion metagenome is used along with KEGG and other protein databases to verify the microbial proteins in the total protein mixture. To derive the host proteins, a similar approach is used based on search against the human genome.
Human subject whole genome sequences	Analysis of the sequence of the host genome using high-throughput DNA sequencing.
Whole exome sequences	Analysis of the protein coding regions of the host genome, which is generally done through sequence analysis.
Whole transcriptome sequences	Sequence-based analysis of RNA transcripts in host tissue using polyA tail separation of eukaryotic transcripts from a mixture of transcripts, converting the RNA to complementary DNA and sequencing the cDNA.
Cytokines	Circulating immune system glycoproteins in blood, plasma, or other bodily fluids are measured through an ELISA assay; data are used as a marker for systemic inflammation.
DNA methylation profiles	Measurement of methylated regions of the host genome. This method uses a combination of restriction enzymes and a reduced representation bisulfite sequencing (RRBS) method to enrich for regions of the genome with cytosine-guanine pairs; these regions are then screened for methylated bases.
Fecal calprotectin proteins	Fecal calprotectin is a protein found in stool, the concentration of which is measured through a standardized immunoassay method and is used to evaluate levels of intestinal inflammation.
Serology	Measurement of antibodies for specific pathogens or protein markers conducted with serum through an ELISA assay.
Human subject contaminating genome sequences	Sequence from total nucleotide extracts from most microbially focused sample types yields a combination of host and microbial sequence data. A computational filtering step, using human genome reference sequence, will separate microbiome from human sequences.
Interactomes	Analysis of protein-protein interactions between members of the microbiota or between the microbiota and the host.
Intestinal epithelial cell profiles	Functional or sequence-based readouts of phenotypes for cell lines derived from primary epithelial cells from individual hosts.
Metabolomes	Measure of metabolomic profiles using untargeted and targeted LC-MS methods.
Lipidomes	Measure of lipid profiles using 2D UPLC-ESI-MS/MS (ultra performance liquid chromatography combined with electrospray ionization tandem mass spectroscopy) with an initial focus on AA (arachidonic acid) and eicosanoids.